How to Remove Bacteria from Drinking Water

Posted by
Brock Robinson on July 16, 2020

Water is one of the earth’s most precious resources. However, as water travels along streams, tunnels through the earth to underground aquifers, or rests in lakes, it is often exposed to bacteria. In fact, before the advent of residential and municipal water disinfection, waterborne diseases were responsible for staggering loss of life. In many developing countries, a lack of access to disinfected water results in tragic, preventable death. 

With many people relying on water from city distributors, fears of waterborne bacteria have decreased. However, for private well owners and those pulling water from unsterilized sources, there is still a very real threat of bacteria residing in their water. With vigilant testing and appropriate water filtration and disinfection in place, bacteria and waterborne pathogens can be eliminated from water, protecting you and your home from disease. 

What bacteria can be found in water?

While water can be home to a wide array of microbiological organisms, protozoa like giardia and cryptosporidium and bacteria like E. coli, shigella, and salmonella are among the organisms that cause the most common concern. Water can also transport viruses, like the rotavirus and the norovirus. Water is the universal solvent, collecting everything from dissolved salts to organic matter and mineral content as it makes its journey from rainwater through the earth to aquifers. 

Fecal matter and animals decaying in the soil can introduce many waterborne pathogens into our water supplies. While not all bacteria present in the water is dangerous, much of it can leave a moldy, algae-like taste or lingering earthy smell to your water. This bacteria is worth removing simply to elevate the quality of water you and your family consume. 

Modern water treatment methods, like chlorination and ultraviolet disinfection, have made huge strides toward eliminating waterborne diseases like typhoid that plagued Western civilization in the early part of the 20th century. However, those with private wells or obtaining water from natural sources need to exercise great caution and utilize water disinfection to make sure the water they consume is potable and free from dangerous pathogens. Private wells are not subject to the same strict government standards for water quality as a municipal distributor. Therefore, it is the duty of well-owners to vigilantly monitor their well and regularly perform water tests to ensure that they are aware of what is present in their water, and taking active measures to keep themselves and their families safe.

Common bacteria found in water:   


Giardia is a microscopic parasite, and one of the most common waterborne disease carriers in both the United States and the world at large. If infected by Giardia, the parasite will dwell in your intestines and cause a condition known as giardiasis. Giardia causes diarrhea, bloating, nausea, and painful stomach cramps.

Giardia is most commonly found in the water of private wells. Giardia gets into the water from human and animal waste. A shallow well is prone to be inundated by rainwaters or flooding. Fecal matter from wild animals can be carried from the soil into wells by precipitation. Wells near farms are especially prone to Giardia infestations, as agricultural runoff from sheep or cows can expose the water to the parasite. Wild animals like beavers, muskrats, and deer can also spread the parasite. Wells polluted by overflowing sewage systems or disrupted septic systems can also become infected with Giardia. Furthermore, if the well has been submerged by floodwater for an extended period of time, there is a greater likelihood the water will contain Giardia. Studies have indicated that Giardia is capable of surviving in very cold waters for extended periods of time.  


Like Giardia, Cryptosporidium is a waterborne microscopic parasite found prevalently around the world. In fact, Giardia and Cryptosporidium (often referred to as just “Crypto”) are the two most common disease-causing waterborne parasites. Cryptosporidium bacteria will reside in the intestine of a human, causing a condition known as cryptosporidiosis. This mild gastrointestinal illness causes diarrhea, dehydration, fever, nausea, and weight loss. For those who possess compromised immune systems or preexisting health conditions, this infection can spread to other areas of the digestive and respiratory tract. When contracted by people with fragile or weakened immunities, cryptosporidiosis can develop into a chronic illness with serious health implications.

Like Giardia, Crypto enters into private wells through floodwaters and rainwaters. Fecal matter from wild animals or runoff from manure used for agricultural purposes can end up in the water supply and contaminate well water with Crypto parasites. Shallow wells or newly bored wells are at greater risk for exposure to Cryptosporidium. The parasite is encased by a hard, protective shell. This allows for Crypto to survive at length outside the body, and also bolsters its defense against traditional chlorination disinfection. However, because of the size of the cyst, it can be reduced by anything smaller than one-micron and certified for cyst removal, as well as other disinfection methods like distillation and ultraviolet.     

E. coli

E coli is a strain of Escherichia coli, bacteria that are found in the intestines of healthy people and animals around the world. While almost all E. coli bacteria are completely harmless, there are a small number of vicious strains that can cause serious illness if consumed. The strain (named O157:H7) is found in the intestines of cattle. This is why E. coli outbreaks are often associated with the consumption of undercooked ground beef or unpasteurized milk. However, E. coli bacteria also contaminate plants, vegetables, and water. Spinach and lettuce exposed to manure from E. coli-carrying cows can become tainted by the disease, and spread it to humans if consumed raw. Furthermore, agricultural runoff, rainwaters, and floods can introduce the dangerous E. coli strain into private wells or lakes and rivers. 

When consumed, E. coli produces a powerful toxin in the lining of the small intestine. This triggers diarrhea, severe stomach cramps, and vomiting. Around 5-10% of E. coli cases develop into a much more complex and serious disease known as HUS (Hemolytic Uremic Syndrome). HUS can lead to permanent kidney damage, or in the most serious incidents, kidney failure. Though there have been a handful of incidents where E. coli was found in municipal water supplies, those most at risk of consuming E. coli through water are those in rural regions with private wells. Since wells are unregulated, and rural areas have more irrigation and agriculture, there is a much higher risk that strains of this nasty bacterium can make its way into your well and contaminate your water. 


Legionella are pathogenic bacteria that thrive in warmer temperature waters and are found naturally in freshwater streams, lakes, and other surface waters. If inhaled, Legionella causes a pneumonia-like illness known as a Legionnaires disease. It is also responsible for a disease called Pontiac Fever, a mild flu-like sickness. Legionella grows faster in warm waters, which can make it more difficult to neutralize with chemical disinfectants like chlorine. 

When Legionella is converted to a mist, it can become incredibly infectious. Hot tubs, showers, baths, humidifiers, and air conditioning units that service large buildings have all been known to spread Legionella. Though less common, you can also contract Legionnaire’s disease by ingesting water with Legionella bacteria.  Diseases caused by inhalation or consumption of legionella can be life-threatening, although most people are able to recover easily with the aid of antibiotics. Legionnaire’s disease presents many of the same symptoms as pneumonia, such as fever, coughing, headaches, and muscle soreness and fatigue.


Shigella are a group of bacteria that spread a highly contagious diarrheal disease called shigellosis. While shigellosis most often spreads among children in schools, daycare centers, or communal pools, adults who drink unfiltered and untreated water are also at risk of contracting the disease. If contracted, the disease causes severe diarrhea, fever, stomach pains, and abdominal cramping.  

Shigella is commonly found in natural water sources, like lakewater, rivers, and streams. This is one of the many reasons drinking water from a natural source, (called “raw water” by some advocates) poses health risks. However, shallow private wells can also harbor the bacteria. Storm runoff, agricultural waste, and broken sewage systems or septic tanks can all spread shigella to your home’s well. Like many waterborne bacteria, shigella makes its way into water sources by human and animal waste. While shigella presents a nasty problem for many well owners, shigellosis is usually contracted recreationally, like swimming in a lake or a poorly maintained pool. 

Explore how to properly test and maintain your pool

well water

How do you remove bacteria from water?

Bacteria can be removed from water through chlorine, UV disinfection, and ozonation. Chlorination is widely used by municipalities to remove bacteria from city water supplies. Many well owners also use chlorine to “shock” their wells and eliminate any bacteria present. UV disinfection systems are also very commonly used by homeowners who depend on well water, as well as many businesses and commercial applications where well water is used or water is drawn from a potentially microbiologically unsafe source. Ozone water treatment can also be found in residential applications, or in commercial settings like kitchens, where fruits and vegetables are washed in high-purity ozonated water.  

If you are looking for a point-of-use method to eliminate viruses and pathogens from your water, bacteria can also be removed from water through water distillation. Water distillers are usually manually-loaded countertop units, though larger, commercial water distillers are also available. 

Bacteria can also be removed from water by bringing water to a rousing boil for at least a full minute. This is why when water pipelines burst or become otherwise compromised, cities issue boil water advisories. During a boil order, homeowners are instructed to boil any water intended for cooking, drinking, or cleaning before usage. This prevents exposure to any bacteria or viruses the water may have become exposed to during the disturbance. 

Some cysts, like Giardia and Cryptosporidium, can be filtered out through mechanical filtration. For example, Giardia cannot pass through a one-micron filter. However, if you are on well water or water otherwise compromised by microorganisms, you should not rely on mechanical filtration alone. The water should be fully disinfected to ensure that you and your home are protected from waterborne diseases. Any filter you do rely on for cyst reduction or removal should be certified by NSF Standard 53 or tested independently against the same standards. This certification confirms that the filter has been tested and approved to reduce or remove contaminants with potential adverse health effects. 

UV Disinfection

One of the most popular, prevalent, and reliable methods of residential bacteria treatment is ultraviolet purification. Ultraviolet light neutralizes the DNA of bacteria, preventing them from reproducing in the water. This renders the bacteria harmless and totally incapable of infecting you or your family members. UV water purification systems generate no waste water, require minimal maintenance, are incredibly effective, and don’t use any chemical additives to purify the water. This makes them generally regarded as one of the best ways to remove biological contaminants from water. 

Water flows into the UV purification system, entering into a chamber where it will be exposed to germicidal ultraviolet light. A thin quartz glass sleeve protects the water from making direct contact with the UV lamp since the water making contact with the electricity would damage the system. The quartz glass sleeve is a transparent barrier, and the ultraviolet light from the lamp radiates through the sleeve. The lamp and sleeve are sealed at the end of the system by protective o-rings, ensuring water is unable to bypass. 

The germicidal properties of the ultraviolet lamp are fueled by tiny balls of mercury in the lamp. As heat is exposed to the lamp, the mercury bulbs emit UV-C rays, debilitating the bacteria in the water and deactivating any microorganisms present. UV lamps provide around 9,000 hours (approximately a year) worth of disinfection. At this time, the lamp is replaced, the quartz sleeve is clean, and the system is ready to continue defending your water supply from pathogenic invaders. A sensor built into the UV system’s ballast will alert you when the lamp is approaching the end of its service life. 

UV systems are ideal for a wide array of homes and applications. Houses that rely on well water, small cottages, vacation homes, and beach houses that draw water from wells all utilize UV disinfection systems to great effect. They are one of the most reliable and preferred methods of whole-house residential water disinfection. They can also be used in RVs. Many off-road adventurers can find themselves in situations where the water source is compromising and could contain bacteria and pathogens. A small UV system fits neatly in most RVs. However, if this is not feasible for your circumstances, a handheld UV purifier, like the SteriPEN, can be used to disinfect smaller quantities of water just as thoroughly as the larger units.

Many businesses and industries also use UV purification to neutralize organisms in their water. Hospitals, laboratories, and manufacturing plants all need sterilized water. Large-scale, industrial UV systems are often employed to purify water for breweries, hydroponic farms and greenhouse agriculture, as well as hospitality services like hotels and food and beverage applications. 

Read more about how UV purification works. | Learn how to maintain your UV system.   


Chlorine is used by water treatment centers across the globe to disinfect water supplies and eliminate waterborne pathogens from drinking water. Chlorine can be easily added at large scales, carefully measured, and behaves predictably, making it a widely popular disinfection choice. When chlorine comes in contact with bacteria, it breaks down the chemical bonds on a molecular level. When chlorine is added to water, a weak acid is formed. This acid, called hypochlorous acid, penetrates the negative charge of bacteria’s cell walls, destroying the microorganism from the inside out. In low and controlled doses, it is harmless to consume. While chlorine does leave a lingering chemical aftertaste to water, the water’s taste can be easily improved by a carbon filter.

Shock chlorination borrows this common water treatment process and applies it to individual private wells. Anytime a new well is bored, a well pump is changed, a well is cleaned, or a well pump is repaired or maintained, you will be advised to shock your well. The term “shock” indicates the addition of a strong dose of a concentrated chlorine solution. In the event of an extreme weather condition, like a flood or storm surge, shock chlorination is recommended to combat any bacteria that may have been introduced to your well. If a well has been left stagnant or unused for a long period of time, chlorination will help to neutralize any bacteria that may have proliferated in the absence of activity. Chlorination can also help to remove bacterial iron from well supplies. While it is extremely effective, shock chlorination will not guarantee perpetual bacterial elimination over the course of the year. It must periodically be performed to keep bacteria and viruses out of the water. Diligent well maintenance and chlorination goes well with the installation of a UV system, as the UV will ensure the water is bacteria-free at all times. 

Chlorine is potent, and other water filtration equipment can become damaged after shock chlorination. A well pressure tank can be cleaned with a more gently chlorinated solution, but those with rubber diaphragms can become damaged by the strong dose of chlorine. These should be bypassed after well chlorination. Similarly, the thin film membrane of a reverse osmosis system can become destroyed by heavy exposure to chlorine. After chlorinating a well, ensure that the RO system is bypassed until after the shock chlorination has run its course. 

Chlorine can also be used to disinfect smaller batches of water at a time. Chlorine tablets are sold to purify individual liters of water at a time. For example, if you are hunting, camping, or fishing, and find yourself in need of fresh, potable water, these tablets can be added to spring water to ensure safe consumption. After a few hours of exposure, the chlorine will have eradicated bacteria, cysts like giardia, and viruses from the water. While this is not a practical usage for the home, these chlorine tablets make a great addition to any wilderness adventure or off-road excursion. They also can be helpful in the event of emergency or boil water advisory. 

Explore how to remove iron from well water. | Learn more about how activated carbon works


Ozone is a powerful and unique water disinfectant. Ozone is extremely germicidal, and rapidly destroys any waterborne viruses and bacteria with nearly unmatched speed. Like chlorine, ozone oxidizes the bacteria and protozoa upon contact. The ozone penetrates the cell walls of the microorganisms, rupturing them on a structural level. Unlike UV disinfection, there is no reduced flow rate or extended contact time required. After shocking a well with chlorine, the chlorine must sit overnight to ensure that it has properly dismantled all the pathogens present in your water supply. Ozone, commonly seen in the house as ozonated faucets, works in a matter of minutes. Ozone is also capable of handily eliminating inorganic matter, as well as micro-pollutants like pesticides and herbicides. Ozone can also eliminate other water contaminants like iron, sulfur, and manganese.

Ozone water treatment uses a generator (or ozonator) to dissolve low concentrations of ozone into your water, usually around 3-5ppm. Ozone (O3) is an oxygen compound with a loosely-bound additional oxygen molecule. Ozone has remarkable oxidation properties, allowing it to quickly and effectively break down bacteria and organic contaminants like iron, manganese, and hydrogen sulfide. Ozone is created naturally in our stratosphere and on the earth, like when lightning strikes. These ozonators simulate this process through electrical discharges that create O3 molecules and release them into the water. 

Ozone has proven to have greater disinfection capabilities than even traditional chlorination, in addition to disinfecting water much faster than chlorine. However, ozone is unstable. Ozone breaks down over the course of around 30 minutes, making it difficult to use city-wide for water treatment. The house at the very end of the municipal water main needs to receive water that has been as thoroughly disinfected as the house closest to the treatment plant, so the lasting stability of chlorine and chloramines make them a more obvious choice.

Ozone is best suited for point-of-use, both in homes and in commercial kitchens. Ozone destroys ethylene gas, which causes fruits and vegetables to wither away, making it ideal for washing produce. It also neutralizes germs found on silverware, plates, and glasses, providing a more thorough cleaning of your dishes. Most important, ozone can destroy over 99.9% of bacteria, viruses, and waterborne pathogens upon contact. If you are using a private water source with elevated total coliform levels or a strong bacterial presence, a more drastic treatment option is required to eliminate the source of the problem. However, an ozone faucet is an extremely effective residential choice for ensuring the water you drink, cook, and clean with is entirely disinfected. 

Ozone is also a remarkable water treatment method for ice machines. Ice machines can be breeding grounds for bacteria, yeast, and mold within the machine. This can lead to pink slime coating the bottom of the machine, discoloring the ice, and risk bacterial exposure to those enjoying the ice. Ozone ice machine sanitation systems treat all water incoming into the machine. This ensures that all of the ice produced by the machine has been treated by O3, completely neutralizing any bacteria present in the water. This leads to a pristine ice machine environment, protecting the ice, the machine and its internal compartments, and even the air within the ice machine's storage bin. Treating ice with ozone will drastically reduce the amount of time devoted to cleaning ice machines. 


Water distillers are a point-of-use water treatment unit that can eliminate bacteria, viruses, and microorganisms from small batches of water at a time. The process of distillation mimics the earth’s hydrologic cycle, the method by which nature itself purifies water. In the hydrologic cycle, water evaporates from the surfaces of lakes, oceans, and rivers. As it transitions from a liquid to a gaseous state, it discards any trace contaminants it has collected, like salts, metals, and particulate matter. Once it rises into the atmosphere, it cools and condenses, forming clouds. It then returns to the earth in a pure, soft, slightly acidic form through precipitation like rain or snow. 

Water distillers replicate this process on a small scale in your own kitchen. Water is loaded into the boiling chamber of the water distiller. A heating element activates, boiling the water until it has converted entirely from a liquid state into steam. The stream travels up through a vented roof in the boiling chamber, and enters into cooling coils. Here, the steam is chilled, causing it to return to a liquid state, and exits the distiller, passing through a carbon post-filter on the way out. The purified, distilled water then collects in a glass or plastic jug, ready to be used. 

Distillation is incredibly effective at eliminating not only bacteria, but contaminants of every kind. Dissolved solids, organics, and ions cannot make the transition into a gaseous state, so they are left behind in the boiling chamber during the distillation process. Viruses, bacteria, and microorganisms cannot survive boiling temperatures, so they are eradicated by the elevated temperatures of the distiller. The only contaminants that can transition from liquid to gas are VOCs, and these are handily removed by the carbon post-filter within the distiller. Water distillation is incredibly effective and is used to treat water in the medical field, laboratories, and in for automotive applications. 

However, if you are concerned that bacteria may be present in your drinking water source (for example, a private well), a water distiller should not be your only recourse. Water distillers are excellent at producing high purity water, but they can only do so in very small batches and very slowly. It takes a countertop water distiller anywhere from 4 to 6 hours to distill a single gallon of water. They also do use an incredible amount of energy, as the heating element and cooling coils must be supplied with energy throughout the duration of the distillation process. Furthermore, you want to avoid bacteria entering any of your home or business’s plumbing. This includes obvious examples like your ice maker, refrigerator, and kitchen sink, but you don’t want to bathe or shower in contaminated water either. There is a high probability of you accidentally ingesting bacteria this way. A water distiller is a fantastic point-of-use solution to remove bacteria, but a whole-house system (like UV and shocking your well) should come before the distiller. 

Learn more about how water distillers work. | Explore if distilled water is actually safe to drink.

Does reverse osmosis remove bacteria? 

Though capable of removing organisms and bacteria, reverse osmosis should not be used as the primary source of removing bacteria. Reverse osmosis systems do not make bacteria reduction claims. Indeed, all reverse osmosis systems will specify in their specs sheets that they are only to be used on potable and microbiologically safe water. Though most bacteria cannot fit through the minute pore size of the reverse osmosis membrane, to preserve the system, bacteria should be eliminated before reaching the reverse osmosis system. It is possible for bacteria to proliferate on the RO membrane. Bacteria can also create pinhole leaks in the membrane, causing deterioration of the membrane and leading to reduced performance and TDS reduction. The o-rings within a residential reverse osmosis system are also not designed to prevent bacteria from migrating, meaning there is a risk of bacteria being reintroduced into your water supply. While reverse osmosis is an incredibly thorough and powerful means of water filtration, the water should be treated by ozonation or UV disinfection before it reaches your RO system. This will help prolong the life of your system and your membrane, as well as ensure you are kept safe from viruses and waterborne pathogens.

Learn more about how reverse osmosis works. | Does your home need a whole-house reverse osmosis system?

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